bosaFS analyses LMER
Pascale Caissy
2021-03-11
20210407: J’ai aouté la date car j’ai retiré les analyses de condition physique étant donné que le type de données qu’on utilise comme variable réponse ne correspond pas vraiment temporellement.
20210415:J’ai encore modifié la date du document, car je veux comparer les modèles avec et sans la longueur standard, qui est un possible downstream effect.
Préparation des données
Méthode de catégorisation des proies :
Utiliser d’abord la taxonomie pour regrouper ensemble;
Vérifier à la fois l’apport en nombre et en % carbone pour chaque catégorie;
Rassembler dans une autre catégorie quand représente < 1 % du carbone et < 5 % du nombre de proies.
Préparation des données par région d’échantillonnage.
## Using region_year as value column: use value.var to override.
Exploration préliminaire
Section 1. Environnement et succès alimentaire
Concernant les mesures de taille spécifiquement, on utilisera les variables log-transformées.
On fera de même avec la mesure de succès alimentaire (feeding_success).
## 2009 2010 2011 2014 2015
## Mackenzie Shelf 12.6857 27.09488 NA 35.40000 31.54290
## Amundsen Gulf Mouth NA NA NA NA 32.85720
## Coronation Maud NA NA 15.59700 NA NA
## Larsen Sound - Victoria Strait NA 11.30658 NA NA NA
## Peel Sound NA 10.81823 17.42556 12.13674 11.36489
## Lancaster Sound NA 13.23085 13.62750 NA 16.59357
## North Water NA NA NA 17.73251 NA
## West Baffin Bay NA NA NA NA 14.48783
## NEG NA NA NA NA NA
## 2016 2017 2018
## Mackenzie Shelf NA NA NA
## Amundsen Gulf Mouth NA NA NA
## Coronation Maud 22.55682 16.26570 14.98442
## Larsen Sound - Victoria Strait 14.74777 NA 11.03090
## Peel Sound 12.85020 NA NA
## Lancaster Sound 17.96064 15.33450 NA
## North Water 20.41569 NA 21.30636
## West Baffin Bay 11.19310 NA NA
## NEG NA 19.12333 NA
## log_est_standard_length sampling_day open_water_day
## log_est_standard_length 1.00 0.40 0.56
## sampling_day 0.40 1.00 0.23
## open_water_day 0.56 0.23 1.00
## prof_mel -0.01 0.10 -0.01
## surf_sal_kgm3 0.18 -0.16 0.46
## surf_temp_degC 0.47 0.04 0.36
## NASC_zoo 0.28 -0.02 0.46
## prof_mel surf_sal_kgm3 surf_temp_degC NASC_zoo
## log_est_standard_length -0.01 0.18 0.47 0.28
## sampling_day 0.10 -0.16 0.04 -0.02
## open_water_day -0.01 0.46 0.36 0.46
## prof_mel 1.00 0.33 -0.36 -0.04
## surf_sal_kgm3 0.33 1.00 -0.17 0.24
## surf_temp_degC -0.36 -0.17 1.00 0.56
## NASC_zoo -0.04 0.24 0.56 1.00
##
## n= 339
##
##
## P
## log_est_standard_length sampling_day open_water_day
## log_est_standard_length 0.0000 0.0000
## sampling_day 0.0000 0.0000
## open_water_day 0.0000 0.0000
## prof_mel 0.8256 0.0652 0.8615
## surf_sal_kgm3 0.0010 0.0027 0.0000
## surf_temp_degC 0.0000 0.4248 0.0000
## NASC_zoo 0.0000 0.7638 0.0000
## prof_mel surf_sal_kgm3 surf_temp_degC NASC_zoo
## log_est_standard_length 0.8256 0.0010 0.0000 0.0000
## sampling_day 0.0652 0.0027 0.4248 0.7638
## open_water_day 0.8615 0.0000 0.0000 0.0000
## prof_mel 0.0000 0.0000 0.4629
## surf_sal_kgm3 0.0000 0.0017 0.0000
## surf_temp_degC 0.0000 0.0017 0.0000
## NASC_zoo 0.4629 0.0000 0.0000
##
## Pearson's product-moment correlation
##
## data: dfish$log_carbon_mg and dfish$log_est_standard_length
## t = 26.732, df = 337, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.7869183 0.8557199
## sample estimates:
## cor
## 0.8243398
##
## Pearson's product-moment correlation
##
## data: dfish$log_feeding_success and dfish$log_est_standard_length
## t = 4.1572, df = 337, p-value = 4.091e-05
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.1171006 0.3198589
## sample estimates:
## cor
## 0.2208648
##
## Pearson's product-moment correlation
##
## data: dfish$log_feeding_success and dfish$log_carbon_mg
## t = 19.851, df = 337, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.6809144 0.7797242
## sample estimates:
## cor
## 0.734183
##
## Pearson's product-moment correlation
##
## data: dfish$fish_cond and dfish$log_est_standard_length
## t = 0.56943, df = 337, p-value = 0.5694
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## -0.07576528 0.13707059
## sample estimates:
## cor
## 0.0310041
##
## Pearson's product-moment correlation
##
## data: dfish$fish_cond and dfish$log_feeding_success
## t = 3.1815, df = 337, p-value = 0.001601
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.06543369 0.27232831
## sample estimates:
## cor
## 0.1707627
La quantité de carbone ingérée est fortement corrélée à la taille des poissons (R = 0.8243398) !
La corrélation entre la taille des poissons et leur succès alimentaire est significative mais bien plus faible (R = 0.2208648) qu’entre la quantité de carbone ingérée et le succès alimentaire (R = cor(dfish$log_carbon_mg,dfish$log_feeding_success)).
Les plus grands poissons n’ont pas nécessairement une meilleure condition physique; la corrélation entre la condition et la taille n’est pas significative (R = 0.0310041).
La corrélation entre le succès alimentaire (mesure à court terme de l’alimentation des poissons) et la condition (mesure intégratrice de l’alimentation des poissons) des individus est significative mais très bruitée (R = 0.1707627).
Succès alimentaire et environnement
Explorations des données
On utilisera la variable log-transformée log_indstandard qui représente la densité de larves filtrées par les filets corrigé en fonction de la profondeur échantillonnée.
La variable NASC_zoo qui représente la concentration de mesozooplankton observée par méthodes acoustiques est problématique : les très fortes valeurs nuisent à des relations linéaires entre variables. On utilisera les valeurs log-transformées.
## log_feeding_success log_indstandard sampling_day
## log_feeding_success 1.00 -0.10 0.13
## log_indstandard -0.10 1.00 -0.24
## sampling_day 0.13 -0.24 1.00
## open_water_day 0.29 -0.07 0.23
## surf_sal_kgm3 0.20 0.35 -0.16
## surf_temp_degC 0.04 -0.42 0.04
## log_NASC_zoo 0.25 -0.09 -0.10
## open_water_day surf_sal_kgm3 surf_temp_degC log_NASC_zoo
## log_feeding_success 0.29 0.20 0.04 0.25
## log_indstandard -0.07 0.35 -0.42 -0.09
## sampling_day 0.23 -0.16 0.04 -0.10
## open_water_day 1.00 0.46 0.36 0.66
## surf_sal_kgm3 0.46 1.00 -0.17 0.35
## surf_temp_degC 0.36 -0.17 1.00 0.49
## log_NASC_zoo 0.66 0.35 0.49 1.00
##
## n= 339
##
##
## P
## log_feeding_success log_indstandard sampling_day
## log_feeding_success 0.0602 0.0168
## log_indstandard 0.0602 0.0000
## sampling_day 0.0168 0.0000
## open_water_day 0.0000 0.1837 0.0000
## surf_sal_kgm3 0.0002 0.0000 0.0027
## surf_temp_degC 0.4284 0.0000 0.4248
## log_NASC_zoo 0.0000 0.1098 0.0702
## open_water_day surf_sal_kgm3 surf_temp_degC log_NASC_zoo
## log_feeding_success 0.0000 0.0002 0.4284 0.0000
## log_indstandard 0.1837 0.0000 0.0000 0.1098
## sampling_day 0.0000 0.0027 0.4248 0.0702
## open_water_day 0.0000 0.0000 0.0000
## surf_sal_kgm3 0.0000 0.0017 0.0000
## surf_temp_degC 0.0000 0.0017 0.0000
## log_NASC_zoo 0.0000 0.0000 0.0000
Modèles de régression linéaire
On va établir les modèles de régression linéaire multiples pour essayer d’expliquer la variabilité du succès alimentaire des poissons échantillonnés.
Lorsque pertinent, nous utiliserons des modèles à effet mixtes aléatoires pour tenir compte de la forte hétérogénéité spatiale de notre échantillonnage.
## Start: AIC=-533.74
## log_feeding_success ~ 1
##
## Df Sum of Sq RSS AIC
## + open_water_day 1 5.7894 64.012 -561.09
## + log_NASC_zoo 1 4.4340 65.368 -553.98
## + log_est_standard_length 1 3.4050 66.397 -548.69
## + surf_sal_kgm3 1 2.7691 67.033 -545.46
## + log_indstandard 1 0.7288 69.073 -535.29
## <none> 69.802 -533.74
## + surf_temp_degC 1 0.1300 69.672 -532.37
##
## Step: AIC=-561.09
## log_feeding_success ~ open_water_day
##
## Df Sum of Sq RSS AIC
## + log_NASC_zoo 1 0.4661 63.546 -561.57
## + log_indstandard 1 0.4643 63.548 -561.56
## + surf_sal_kgm3 1 0.3906 63.622 -561.16
## <none> 64.012 -561.09
## + log_est_standard_length 1 0.3559 63.656 -560.98
## + surf_temp_degC 1 0.2796 63.733 -560.57
## - open_water_day 1 5.7894 69.802 -533.74
##
## Step: AIC=-561.57
## log_feeding_success ~ open_water_day + log_NASC_zoo
##
## Df Sum of Sq RSS AIC
## + surf_temp_degC 1 0.70654 62.840 -563.36
## + log_est_standard_length 1 0.47609 63.070 -562.11
## + log_indstandard 1 0.41805 63.128 -561.80
## <none> 63.546 -561.57
## + surf_sal_kgm3 1 0.34092 63.205 -561.39
## - log_NASC_zoo 1 0.46611 64.012 -561.09
## - open_water_day 1 1.82156 65.368 -553.98
##
## Step: AIC=-563.36
## log_feeding_success ~ open_water_day + log_NASC_zoo + surf_temp_degC
##
## Df Sum of Sq RSS AIC
## + log_est_standard_length 1 1.36284 61.477 -568.79
## + log_indstandard 1 1.26168 61.578 -568.23
## <none> 62.840 -563.36
## + surf_sal_kgm3 1 0.05008 62.789 -561.63
## - surf_temp_degC 1 0.70654 63.546 -561.57
## - log_NASC_zoo 1 0.89305 63.733 -560.57
## - open_water_day 1 1.91649 64.756 -555.17
##
## Step: AIC=-568.79
## log_feeding_success ~ open_water_day + log_NASC_zoo + surf_temp_degC +
## log_est_standard_length
##
## Df Sum of Sq RSS AIC
## + log_indstandard 1 0.94848 60.528 -572.06
## - open_water_day 1 0.28459 61.761 -569.22
## <none> 61.477 -568.79
## + surf_sal_kgm3 1 0.00769 61.469 -566.83
## - log_est_standard_length 1 1.36284 62.840 -563.36
## - log_NASC_zoo 1 1.55894 63.036 -562.30
## - surf_temp_degC 1 1.59330 63.070 -562.11
##
## Step: AIC=-572.06
## log_feeding_success ~ open_water_day + log_NASC_zoo + surf_temp_degC +
## log_est_standard_length + log_indstandard
##
## Df Sum of Sq RSS AIC
## <none> 60.528 -572.06
## - open_water_day 1 0.36350 60.892 -572.03
## + surf_sal_kgm3 1 0.17554 60.353 -571.04
## - log_indstandard 1 0.94848 61.477 -568.79
## - log_est_standard_length 1 1.04964 61.578 -568.23
## - log_NASC_zoo 1 1.74647 62.275 -564.42
## - surf_temp_degC 1 2.32827 62.856 -561.26## Step Df Deviance Resid. Df Resid. Dev AIC
## 1 NA NA 338 69.80162 -533.7363
## 2 + open_water_day -1 5.7894295 337 64.01219 -561.0881
## 3 + log_NASC_zoo -1 0.4661140 336 63.54607 -561.5656
## 4 + surf_temp_degC -1 0.7065431 335 62.83953 -563.3560
## 5 + log_est_standard_length -1 1.3628423 334 61.47669 -568.7890
## 6 + log_indstandard -1 0.9484775 333 60.52821 -572.0599##
## Call:
## lm(formula = log_feeding_success ~ open_water_day + log_NASC_zoo +
## surf_temp_degC + log_est_standard_length + log_indstandard,
## data = dfish)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.60153 -0.22605 0.05541 0.29417 1.05801
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.607910 0.190789 -18.910 < 2e-16 ***
## open_water_day 0.001521 0.001075 1.414 0.158253
## log_NASC_zoo 0.175156 0.056507 3.100 0.002102 **
## surf_temp_degC -0.048791 0.013633 -3.579 0.000396 ***
## log_est_standard_length 0.444870 0.185127 2.403 0.016806 *
## log_indstandard -0.078218 0.034241 -2.284 0.022982 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4263 on 333 degrees of freedom
## Multiple R-squared: 0.1329, Adjusted R-squared: 0.1198
## F-statistic: 10.2 on 5 and 333 DF, p-value: 4.13e-09## open_water_day log_NASC_zoo surf_temp_degC
## 2.537153 2.277807 1.864444
## log_est_standard_length log_indstandard
## 1.860411 1.265789
Les conditions environnementales expliquent mal la variabilité du succès d’alimentation.
Seulement la taille, la température de surface, l’abondance de larves, l’abondance de macrozooplancton révélée par l’acoustique et le nombre de jours depuis la débâcle des poissons explique < 10 % de la variance observée (\(R^2\) = 0.1198335)
On va maintenant tester avec un modèle qui n’inclut pas la taille, qui pourrait être considérée comme un “downstream effect” selon certains contextes
## Start: AIC=-533.74
## log_feeding_success ~ 1
##
## Df Sum of Sq RSS AIC
## + open_water_day 1 5.7894 64.012 -561.09
## + log_NASC_zoo 1 4.4340 65.368 -553.98
## + surf_sal_kgm3 1 2.7691 67.033 -545.46
## + log_indstandard 1 0.7288 69.073 -535.29
## <none> 69.802 -533.74
## + surf_temp_degC 1 0.1300 69.672 -532.37
##
## Step: AIC=-561.09
## log_feeding_success ~ open_water_day
##
## Df Sum of Sq RSS AIC
## + log_NASC_zoo 1 0.4661 63.546 -561.57
## + log_indstandard 1 0.4643 63.548 -561.56
## + surf_sal_kgm3 1 0.3906 63.622 -561.16
## <none> 64.012 -561.09
## + surf_temp_degC 1 0.2796 63.733 -560.57
## - open_water_day 1 5.7894 69.802 -533.74
##
## Step: AIC=-561.57
## log_feeding_success ~ open_water_day + log_NASC_zoo
##
## Df Sum of Sq RSS AIC
## + surf_temp_degC 1 0.70654 62.840 -563.36
## + log_indstandard 1 0.41805 63.128 -561.80
## <none> 63.546 -561.57
## + surf_sal_kgm3 1 0.34092 63.205 -561.39
## - log_NASC_zoo 1 0.46611 64.012 -561.09
## - open_water_day 1 1.82156 65.368 -553.98
##
## Step: AIC=-563.36
## log_feeding_success ~ open_water_day + log_NASC_zoo + surf_temp_degC
##
## Df Sum of Sq RSS AIC
## + log_indstandard 1 1.26168 61.578 -568.23
## <none> 62.840 -563.36
## + surf_sal_kgm3 1 0.05008 62.789 -561.63
## - surf_temp_degC 1 0.70654 63.546 -561.57
## - log_NASC_zoo 1 0.89305 63.733 -560.57
## - open_water_day 1 1.91649 64.756 -555.17
##
## Step: AIC=-568.23
## log_feeding_success ~ open_water_day + log_NASC_zoo + surf_temp_degC +
## log_indstandard
##
## Df Sum of Sq RSS AIC
## <none> 61.578 -568.23
## + surf_sal_kgm3 1 0.34054 61.237 -568.11
## - log_NASC_zoo 1 1.15837 62.736 -563.91
## - log_indstandard 1 1.26168 62.840 -563.36
## - surf_temp_degC 1 1.55017 63.128 -561.80
## - open_water_day 1 1.91256 63.490 -559.86## Step Df Deviance Resid. Df Resid. Dev AIC
## 1 NA NA 338 69.80162 -533.7363
## 2 + open_water_day -1 5.7894295 337 64.01219 -561.0881
## 3 + log_NASC_zoo -1 0.4661140 336 63.54607 -561.5656
## 4 + surf_temp_degC -1 0.7065431 335 62.83953 -563.3560
## 5 + log_indstandard -1 1.2616830 334 61.57785 -568.2316##
## Call:
## lm(formula = log_feeding_success ~ open_water_day + log_NASC_zoo +
## surf_temp_degC + log_indstandard, data = dfish)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.65508 -0.23667 0.05148 0.29186 1.06973
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.1732285 0.0610967 -51.938 < 2e-16 ***
## open_water_day 0.0029264 0.0009086 3.221 0.00140 **
## log_NASC_zoo 0.1368568 0.0545987 2.507 0.01266 *
## surf_temp_degC -0.0372677 0.0128523 -2.900 0.00398 **
## log_indstandard -0.0893786 0.0341663 -2.616 0.00930 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4294 on 334 degrees of freedom
## Multiple R-squared: 0.1178, Adjusted R-squared: 0.1073
## F-statistic: 11.15 on 4 and 334 DF, p-value: 1.674e-08##
## Call:
## lm(formula = log_feeding_success ~ open_water_day + log_NASC_zoo +
## surf_temp_degC + log_est_standard_length + log_indstandard,
## data = dfish)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.60153 -0.22605 0.05541 0.29417 1.05801
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.607910 0.190789 -18.910 < 2e-16 ***
## open_water_day 0.001521 0.001075 1.414 0.158253
## log_NASC_zoo 0.175156 0.056507 3.100 0.002102 **
## surf_temp_degC -0.048791 0.013633 -3.579 0.000396 ***
## log_est_standard_length 0.444870 0.185127 2.403 0.016806 *
## log_indstandard -0.078218 0.034241 -2.284 0.022982 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4263 on 333 degrees of freedom
## Multiple R-squared: 0.1329, Adjusted R-squared: 0.1198
## F-statistic: 10.2 on 5 and 333 DF, p-value: 4.13e-09## open_water_day log_NASC_zoo surf_temp_degC log_indstandard
## 1.786072 2.096606 1.633757 1.242500
## Start: AIC=-533.74
## log_feeding_success ~ 1
##
## Df Sum of Sq RSS AIC
## + log_NASC_zoo 1 4.4340 65.368 -553.98
## + log_est_standard_length 1 3.4050 66.397 -548.69
## + surf_sal_kgm3 1 2.7691 67.033 -545.46
## + log_indstandard 1 0.7288 69.073 -535.29
## <none> 69.802 -533.74
## + surf_temp_degC 1 0.1300 69.672 -532.37
##
## Step: AIC=-553.98
## log_feeding_success ~ log_NASC_zoo
##
## Df Sum of Sq RSS AIC
## + log_est_standard_length 1 1.6519 63.716 -560.66
## + surf_sal_kgm3 1 0.9919 64.376 -557.17
## + surf_temp_degC 1 0.6116 64.756 -555.17
## + log_indstandard 1 0.4530 64.915 -554.34
## <none> 65.368 -553.98
## - log_NASC_zoo 1 4.4340 69.802 -533.74
##
## Step: AIC=-560.66
## log_feeding_success ~ log_NASC_zoo + log_est_standard_length
##
## Df Sum of Sq RSS AIC
## + surf_temp_degC 1 1.95445 61.761 -569.22
## + surf_sal_kgm3 1 0.79173 62.924 -562.90
## <none> 63.716 -560.66
## + log_indstandard 1 0.11840 63.597 -559.29
## - log_est_standard_length 1 1.65191 65.368 -553.98
## - log_NASC_zoo 1 2.68088 66.397 -548.69
##
## Step: AIC=-569.22
## log_feeding_success ~ log_NASC_zoo + log_est_standard_length +
## surf_temp_degC
##
## Df Sum of Sq RSS AIC
## + log_indstandard 1 0.8696 60.892 -572.03
## <none> 61.761 -569.22
## + surf_sal_kgm3 1 0.0536 61.708 -567.52
## - surf_temp_degC 1 1.9545 63.716 -560.66
## - log_est_standard_length 1 2.9947 64.756 -555.17
## - log_NASC_zoo 1 4.3041 66.065 -548.39
##
## Step: AIC=-572.03
## log_feeding_success ~ log_NASC_zoo + log_est_standard_length +
## surf_temp_degC + log_indstandard
##
## Df Sum of Sq RSS AIC
## <none> 60.892 -572.03
## + surf_sal_kgm3 1 0.3192 60.572 -571.81
## - log_indstandard 1 0.8696 61.761 -569.22
## - log_est_standard_length 1 2.5987 63.490 -559.86
## - surf_temp_degC 1 2.7056 63.597 -559.29
## - log_NASC_zoo 1 4.8317 65.723 -548.14## Step Df Deviance Resid. Df Resid. Dev AIC
## 1 NA NA 338 69.80162 -533.7363
## 2 + log_NASC_zoo -1 4.433986 337 65.36763 -553.9848
## 3 + log_est_standard_length -1 1.651905 336 63.71572 -560.6618
## 4 + surf_temp_degC -1 1.954451 335 61.76127 -569.2233
## 5 + log_indstandard -1 0.869567 334 60.89171 -572.0302##
## Call:
## lm(formula = log_feeding_success ~ log_NASC_zoo + log_est_standard_length +
## surf_temp_degC + log_indstandard, data = dfish)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.6019 -0.2335 0.0534 0.2840 1.0369
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.71463 0.17549 -21.167 < 2e-16 ***
## log_NASC_zoo 0.22569 0.04384 5.148 4.5e-07 ***
## log_est_standard_length 0.58731 0.15556 3.775 0.000189 ***
## surf_temp_degC -0.05191 0.01347 -3.852 0.000140 ***
## log_indstandard -0.07469 0.03420 -2.184 0.029660 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.427 on 334 degrees of freedom
## Multiple R-squared: 0.1276, Adjusted R-squared: 0.1172
## F-statistic: 12.22 on 4 and 334 DF, p-value: 2.782e-09##
## Call:
## lm(formula = log_feeding_success ~ open_water_day + log_NASC_zoo +
## surf_temp_degC + log_indstandard, data = dfish)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.65508 -0.23667 0.05148 0.29186 1.06973
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.1732285 0.0610967 -51.938 < 2e-16 ***
## open_water_day 0.0029264 0.0009086 3.221 0.00140 **
## log_NASC_zoo 0.1368568 0.0545987 2.507 0.01266 *
## surf_temp_degC -0.0372677 0.0128523 -2.900 0.00398 **
## log_indstandard -0.0893786 0.0341663 -2.616 0.00930 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4294 on 334 degrees of freedom
## Multiple R-squared: 0.1178, Adjusted R-squared: 0.1073
## F-statistic: 11.15 on 4 and 334 DF, p-value: 1.674e-08##
## Call:
## lm(formula = log_feeding_success ~ open_water_day + log_NASC_zoo +
## surf_temp_degC + log_est_standard_length + log_indstandard,
## data = dfish)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.60153 -0.22605 0.05541 0.29417 1.05801
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.607910 0.190789 -18.910 < 2e-16 ***
## open_water_day 0.001521 0.001075 1.414 0.158253
## log_NASC_zoo 0.175156 0.056507 3.100 0.002102 **
## surf_temp_degC -0.048791 0.013633 -3.579 0.000396 ***
## log_est_standard_length 0.444870 0.185127 2.403 0.016806 *
## log_indstandard -0.078218 0.034241 -2.284 0.022982 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4263 on 333 degrees of freedom
## Multiple R-squared: 0.1329, Adjusted R-squared: 0.1198
## F-statistic: 10.2 on 5 and 333 DF, p-value: 4.13e-09## open_water_day log_NASC_zoo surf_temp_degC log_indstandard
## 1.786072 2.096606 1.633757 1.242500
Quand on inclut la taille, on enlève l’effet de la date de débâcle, ce qui semble suggérer que ces larves bénéficient d’une plus longue saison de croissance. Le modèle plus rigoureux demeure celui où on inclut toutes les variables: bien que OWD semble avoir un effet marginal, son ajout rend le modèle plus rigoureux, car cela donne une idée des conditions de glace au moment de l’échantillonnage et de l’avancement général de la saison estivale dans le système.
On va maintenant vérifier avec des modèles mixtes l’influence possible de l’hétérogénéité régionale.
## boundary (singular) fit: see ?isSingular## Warning: Model failed to converge with 1 negative eigenvalue: -1.8e+00## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log_feeding_success ~ log_est_standard_length + log_indstandard +
## surf_temp_degC + open_water_day + log_NASC_zoo + (log_est_standard_length +
## log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo |
## region)
## Data: dfish.LMER
##
## REML criterion at convergence: 325.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1787 -0.5515 0.1145 0.6706 2.6566
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 5.381e-01 0.733537
## log_est_standard_length 9.167e-02 0.302777 -1.00
## log_indstandard 4.313e-02 0.207686 0.96 -0.97
## surf_temp_degC 4.563e-04 0.021362 1.00 -1.00 0.97
## open_water_day 1.934e-05 0.004397 0.90 -0.91 0.98 0.91
## log_NASC_zoo 2.226e-01 0.471791 -0.99 0.99 -0.98 -0.99
## Residual 1.419e-01 0.376706
##
##
##
##
##
##
## -0.93
##
## Number of obs: 314, groups: region, 7
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -3.818588 0.341032 5.422360 -11.197 5.94e-05 ***
## log_est_standard_length 0.739721 0.209375 12.346991 3.533 0.00396 **
## log_indstandard -0.099716 0.090853 4.594619 -1.098 0.32656
## surf_temp_degC -0.039446 0.016071 3.226979 -2.455 0.08532 .
## open_water_day -0.003101 0.002163 4.489234 -1.434 0.21747
## log_NASC_zoo 0.364785 0.195499 3.628274 1.866 0.14276
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ lg_nds srf__C opn_w_
## lg_st_stnd_ -0.861
## lg_ndstndrd 0.758 -0.399
## srf_tmp_dgC 0.534 -0.512 0.485
## open_wtr_dy 0.624 -0.583 0.649 0.420
## log_NASC_zo -0.785 0.549 -0.812 -0.588 -0.815
## convergence code: 0
## boundary (singular) fit: see ?isSingular## # Intraclass Correlation Coefficient
##
## Adjusted ICC: 0.287
## Conditional ICC: 0.244## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 2.58409 (tol = 0.002, component 1)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 1.89395 (tol = 0.002, component 1)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 1.41816 (tol = 0.002, component 1)## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular## Warning: Model failed to converge with 1 negative eigenvalue: -2.4e+00## ANOVA-like table for random-effects: Single term deletions
##
## Model:
## log_feeding_success ~ log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo + (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region)
## npar
## <none> 28
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 22
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 22
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 22
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 22
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 22
## logLik
## <none> -162.60
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) -165.73
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) -171.52
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) -163.85
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) -163.79
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) -173.88
## AIC
## <none> 381.20
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 375.47
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 387.04
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 371.70
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 371.59
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 391.75
## LRT
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 6.2688
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 17.8483
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 2.5043
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 2.3942
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 22.5536
## Df
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 6
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 6
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 6
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 6
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 6
## Pr(>Chisq)
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 0.3937594
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 0.0066228
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 0.8679866
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 0.8801118
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) 0.0009606
##
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region)
## log_indstandard in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) **
## surf_temp_degC in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region)
## open_water_day in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region)
## log_NASC_zoo in (log_est_standard_length + log_indstandard + surf_temp_degC + open_water_day + log_NASC_zoo | region) ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0222128 (tol = 0.002, component 1)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log_feeding_success ~ log_est_standard_length + open_water_day +
## surf_temp_degC + log_NASC_zoo + log_indstandard + (log_NASC_zoo +
## log_indstandard | region)
## Data: dfish.LMER
##
## REML criterion at convergence: 333.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.2687 -0.5095 0.1223 0.6485 2.7144
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 0.32376 0.5690
## log_NASC_zoo 0.12394 0.3521 -1.00
## log_indstandard 0.05281 0.2298 1.00 -1.00
## Residual 0.14694 0.3833
## Number of obs: 314, groups: region, 7
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -3.901386 0.289210 10.916720 -13.490 3.77e-08 ***
## log_est_standard_length 0.761345 0.178531 294.430005 4.264 2.70e-05 ***
## open_water_day -0.001886 0.001366 70.473731 -1.381 0.17171
## surf_temp_degC -0.042853 0.012974 178.417013 -3.303 0.00116 **
## log_NASC_zoo 0.304681 0.151616 5.984454 2.010 0.09133 .
## log_indstandard -0.138772 0.098512 5.226358 -1.409 0.21555
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ opn_w_ srf__C l_NASC
## lg_st_stnd_ -0.563
## open_wtr_dy 0.113 -0.416
## srf_tmp_dgC 0.173 -0.326 0.134
## log_NASC_zo -0.733 0.070 -0.297 -0.158
## lg_ndstndrd 0.741 0.084 -0.037 0.101 -0.859
## convergence code: 0
## Model failed to converge with max|grad| = 0.0222128 (tol = 0.002, component 1)## # Intraclass Correlation Coefficient
##
## Adjusted ICC: 0.317
## Conditional ICC: 0.270## Warning in checkMatrixPackageVersion(): Package version inconsistency detected.
## TMB was built with Matrix version 1.3.2
## Current Matrix version is 1.2.18
## Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package## [[1]]## `geom_smooth()` using formula 'y ~ x'
##
## [[2]]
## [[2]]$region## `geom_smooth()` using formula 'y ~ x'
##
##
## [[3]]
##
## [[4]]## `geom_smooth()` using formula 'y ~ x'
Ajouter les régions comme effet aléatoire est plus rigoureux d’un point de vue de l’analyse de nos résultats, et cela permet de tenir compte de la variabilité de l’effet des variables explicatives sur le succès alimentaire selon les régions, en particulier de la densité de zooplancton observée par l’acoustique qui démontre des effets parfois inverses.
SANS MS 2010: Modèles de succès alimentaire
Modèles de régression linéaire
On va établir les modèles de régression linéaire multiples pour essayer d’expliquer la variabilité du succès alimentaire des poissons échantillonnés.
Lorsque pertinent, nous utiliserons des modèles à effet mixtes aléatoires pour tenir compte de la forte hétérogénéité spatiale de notre échantillonnage.
## Start: AIC=-521.94
## log_feeding_success ~ 1
##
## Df Sum of Sq RSS AIC
## + log_NASC_zoo 1 9.0891 54.697 -569.60
## + open_water_day 1 7.3332 56.453 -559.39
## + log_est_standard_length 1 6.0368 57.749 -552.06
## + surf_temp_degC 1 2.5523 61.234 -533.13
## + surf_sal_kgm3 1 2.3246 61.462 -531.93
## + log_indstandard 1 1.1629 62.623 -525.89
## <none> 63.786 -521.94
##
## Step: AIC=-569.6
## log_feeding_success ~ log_NASC_zoo
##
## Df Sum of Sq RSS AIC
## + log_est_standard_length 1 3.4014 51.296 -588.33
## + open_water_day 1 0.8995 53.798 -572.95
## + log_indstandard 1 0.8817 53.815 -572.85
## <none> 54.697 -569.60
## + surf_temp_degC 1 0.2581 54.439 -569.12
## + surf_sal_kgm3 1 0.0965 54.601 -568.17
## - log_NASC_zoo 1 9.0891 63.786 -521.94
##
## Step: AIC=-588.33
## log_feeding_success ~ log_NASC_zoo + log_est_standard_length
##
## Df Sum of Sq RSS AIC
## <none> 51.296 -588.33
## + log_indstandard 1 0.2139 51.082 -587.68
## + surf_temp_degC 1 0.0293 51.266 -586.52
## + open_water_day 1 0.0118 51.284 -586.41
## + surf_sal_kgm3 1 0.0033 51.292 -586.36
## - log_est_standard_length 1 3.4014 54.697 -569.60
## - log_NASC_zoo 1 6.4537 57.749 -552.06## Step Df Deviance Resid. Df Resid. Dev AIC
## 1 NA NA 322 63.78620 -521.9433
## 2 + log_NASC_zoo -1 9.089109 321 54.69710 -569.5969
## 3 + log_est_standard_length -1 3.401368 320 51.29573 -588.3345##
## Call:
## lm(formula = log_feeding_success ~ log_NASC_zoo + log_est_standard_length,
## data = dfish_noMS2010)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.56536 -0.20871 0.06758 0.25927 1.07335
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.78461 0.16358 -23.136 < 2e-16 ***
## log_NASC_zoo 0.24667 0.03888 6.345 7.59e-10 ***
## log_est_standard_length 0.63377 0.13758 4.606 5.92e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4004 on 320 degrees of freedom
## Multiple R-squared: 0.1958, Adjusted R-squared: 0.1908
## F-statistic: 38.96 on 2 and 320 DF, p-value: 7.19e-16## log_NASC_zoo log_est_standard_length
## 1.049865 1.049865
Les conditions environnementales expliquent mal la variabilité du succès d’alimentation.
Seulement l’abondance de larves, l’abondance de macrozooplancton révélée par l’acoustique et le nombre de jours depuis la débâcle des poissons explique 16 % de la variance observée (\(R^2\) = 0.1907917)
On va maintenant vérifier avec des modèles mixtes l’influence possible de l’hétérogénéité régionale.
## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0427396 (tol = 0.002, component 1)## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log_feeding_success ~ log_est_standard_length + log_NASC_zoo +
## (log_est_standard_length + log_NASC_zoo | region)
## Data: dfish.LMER2
##
## REML criterion at convergence: 325
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6966 -0.4692 0.0435 0.6518 2.6626
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 0.12479 0.3533
## log_est_standard_length 0.05814 0.2411 -1.00
## log_NASC_zoo 0.04889 0.2211 -0.23 0.20
## Residual 0.14822 0.3850
## Number of obs: 323, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -3.73869 0.21969 5.84323 -17.018 3.35e-06 ***
## log_est_standard_length 0.62756 0.17192 7.55483 3.650 0.00716 **
## log_NASC_zoo 0.27346 0.09317 4.57230 2.935 0.03615 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__
## lg_st_stnd_ -0.979
## log_NASC_zo -0.044 -0.045
## convergence code: 0
## Model failed to converge with max|grad| = 0.0427396 (tol = 0.002, component 1)## # Intraclass Correlation Coefficient
##
## Adjusted ICC: 0.159
## Conditional ICC: 0.127## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0142665 (tol = 0.002, component 1)## ANOVA-like table for random-effects: Single term deletions
##
## Model:
## log_feeding_success ~ log_est_standard_length + log_NASC_zoo + (log_est_standard_length + log_NASC_zoo | region)
## npar
## <none> 10
## log_est_standard_length in (log_est_standard_length + log_NASC_zoo | region) 7
## log_NASC_zoo in (log_est_standard_length + log_NASC_zoo | region) 7
## logLik
## <none> -162.52
## log_est_standard_length in (log_est_standard_length + log_NASC_zoo | region) -162.80
## log_NASC_zoo in (log_est_standard_length + log_NASC_zoo | region) -164.10
## AIC
## <none> 345.03
## log_est_standard_length in (log_est_standard_length + log_NASC_zoo | region) 339.59
## log_NASC_zoo in (log_est_standard_length + log_NASC_zoo | region) 342.20
## LRT
## <none>
## log_est_standard_length in (log_est_standard_length + log_NASC_zoo | region) 0.5586
## log_NASC_zoo in (log_est_standard_length + log_NASC_zoo | region) 3.1686
## Df
## <none>
## log_est_standard_length in (log_est_standard_length + log_NASC_zoo | region) 3
## log_NASC_zoo in (log_est_standard_length + log_NASC_zoo | region) 3
## Pr(>Chisq)
## <none>
## log_est_standard_length in (log_est_standard_length + log_NASC_zoo | region) 0.9058
## log_NASC_zoo in (log_est_standard_length + log_NASC_zoo | region) 0.3664## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: log_feeding_success ~ log_est_standard_length + log_NASC_zoo +
## (1 | region)
## Data: dfish.LMER2
##
## REML criterion at convergence: 328.2
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.7751 -0.5470 0.0552 0.6522 2.7162
##
## Random effects:
## Groups Name Variance Std.Dev.
## region (Intercept) 0.01505 0.1227
## Residual 0.15205 0.3899
## Number of obs: 323, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -3.86650 0.19559 97.21200 -19.769 < 2e-16 ***
## log_est_standard_length 0.69047 0.15677 168.99490 4.404 1.88e-05 ***
## log_NASC_zoo 0.32936 0.05596 46.46065 5.886 4.16e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__
## lg_st_stnd_ -0.963
## log_NASC_zo 0.003 -0.121## # Intraclass Correlation Coefficient
##
## Adjusted ICC: 0.090
## Conditional ICC: 0.066## [[1]]## `geom_smooth()` using formula 'y ~ x'
##
## [[2]]
## [[2]]$region## `geom_smooth()` using formula 'y ~ x'
##
##
## [[3]]
##
## [[4]]## `geom_smooth()` using formula 'y ~ x'
## # Explained Variance by Level
##
## Level | R2
## ---------------
## Level 1 | 0.153
## region | 0.277
Section 2. Proies et succès alimentaire
Succès alimentaire et nature quantitative des proies
On explore les relations possibles entre le succès alimentaire et la taille des proies, leur nombre et leur diversité.
## log_feeding_success log_prey_max_um log_prey_min_um
## log_feeding_success 1.00 -0.14 -0.04
## log_prey_max_um -0.14 1.00 0.16
## log_prey_min_um -0.04 0.16 1.00
## log_prey_median_um -0.18 0.58 0.48
## log_prey_range_um -0.14 0.99 0.06
## log_total_preys -0.16 0.03 -0.03
## log_est_standard_length 0.22 -0.20 -0.03
## log_prey_median_um log_prey_range_um log_total_preys
## log_feeding_success -0.18 -0.14 -0.16
## log_prey_max_um 0.58 0.99 0.03
## log_prey_min_um 0.48 0.06 -0.03
## log_prey_median_um 1.00 0.54 0.00
## log_prey_range_um 0.54 1.00 0.04
## log_total_preys 0.00 0.04 1.00
## log_est_standard_length -0.09 -0.21 -0.07
## log_est_standard_length
## log_feeding_success 0.22
## log_prey_max_um -0.20
## log_prey_min_um -0.03
## log_prey_median_um -0.09
## log_prey_range_um -0.21
## log_total_preys -0.07
## log_est_standard_length 1.00
##
## n= 339
##
##
## P
## log_feeding_success log_prey_max_um log_prey_min_um
## log_feeding_success 0.0075 0.4818
## log_prey_max_um 0.0075 0.0030
## log_prey_min_um 0.4818 0.0030
## log_prey_median_um 0.0007 0.0000 0.0000
## log_prey_range_um 0.0077 0.0000 0.3091
## log_total_preys 0.0025 0.5502 0.5353
## log_est_standard_length 0.0000 0.0002 0.5924
## log_prey_median_um log_prey_range_um log_total_preys
## log_feeding_success 0.0007 0.0077 0.0025
## log_prey_max_um 0.0000 0.0000 0.5502
## log_prey_min_um 0.0000 0.3091 0.5353
## log_prey_median_um 0.0000 0.9533
## log_prey_range_um 0.0000 0.5004
## log_total_preys 0.9533 0.5004
## log_est_standard_length 0.1121 0.0001 0.1831
## log_est_standard_length
## log_feeding_success 0.0000
## log_prey_max_um 0.0002
## log_prey_min_um 0.5924
## log_prey_median_um 0.1121
## log_prey_range_um 0.0001
## log_total_preys 0.1831
## log_est_standard_length
Modèles de régression linéaire
On va établir les modèles de régression linéaire multiples pour essayer d’expliquer la variabilité du succes d’alimentation des poissons échantillonnés selon les propriétés de leur alimentation.
## Start: AIC=-533.74
## log_feeding_success ~ 1
##
## Df Sum of Sq RSS AIC
## + log_est_standard_length 1 3.4050 66.397 -548.69
## + shannon 1 3.3105 66.491 -548.21
## + log_prey_median_um 1 2.3678 67.434 -543.44
## + log_total_preys 1 1.8689 67.933 -540.94
## + log_prey_max_um 1 1.4671 68.335 -538.94
## <none> 69.802 -533.74
##
## Step: AIC=-548.69
## log_feeding_success ~ log_est_standard_length
##
## Df Sum of Sq RSS AIC
## + log_prey_median_um 1 1.9167 64.480 -556.62
## + log_total_preys 1 1.5292 64.867 -554.59
## + shannon 1 1.0753 65.321 -552.23
## + log_prey_max_um 1 0.7376 65.659 -550.48
## <none> 66.397 -548.69
## - log_est_standard_length 1 3.4050 69.802 -533.74
##
## Step: AIC=-556.62
## log_feeding_success ~ log_est_standard_length + log_prey_median_um
##
## Df Sum of Sq RSS AIC
## + log_total_preys 1 1.53983 62.940 -562.81
## + shannon 1 0.95548 63.524 -559.68
## <none> 64.480 -556.62
## + log_prey_max_um 1 0.00496 64.475 -554.65
## - log_prey_median_um 1 1.91671 66.397 -548.69
## - log_est_standard_length 1 2.95389 67.434 -543.44
##
## Step: AIC=-562.81
## log_feeding_success ~ log_est_standard_length + log_prey_median_um +
## log_total_preys
##
## Df Sum of Sq RSS AIC
## + shannon 1 0.89242 62.048 -565.66
## <none> 62.940 -562.81
## + log_prey_max_um 1 0.00157 62.938 -560.82
## - log_total_preys 1 1.53983 64.480 -556.62
## - log_prey_median_um 1 1.92732 64.867 -554.59
## - log_est_standard_length 1 2.63817 65.578 -550.89
##
## Step: AIC=-565.66
## log_feeding_success ~ log_est_standard_length + log_prey_median_um +
## log_total_preys + shannon
##
## Df Sum of Sq RSS AIC
## <none> 62.048 -565.66
## + log_prey_max_um 1 0.00157 62.046 -563.66
## - shannon 1 0.89242 62.940 -562.81
## - log_est_standard_length 1 0.89618 62.944 -562.79
## - log_total_preys 1 1.47676 63.524 -559.68
## - log_prey_median_um 1 1.81071 63.858 -557.90## Step Df Deviance Resid. Df Resid. Dev AIC
## 1 NA NA 338 69.80162 -533.7363
## 2 + log_est_standard_length -1 3.4050113 337 66.39660 -548.6901
## 3 + log_prey_median_um -1 1.9167128 336 64.47989 -556.6202
## 4 + log_total_preys -1 1.5398314 335 62.94006 -562.8141
## 5 + shannon -1 0.8924158 334 62.04764 -565.6551##
## Call:
## lm(formula = log_feeding_success ~ log_est_standard_length +
## log_prey_median_um + log_total_preys + shannon, data = prey_matrix_comb2)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.33580 -0.24354 0.03315 0.29649 0.98975
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -2.47662 0.33593 -7.372 1.33e-12 ***
## log_est_standard_length 0.34871 0.15876 2.196 0.02875 *
## log_prey_median_um -0.33100 0.10602 -3.122 0.00195 **
## log_total_preys -0.13647 0.04840 -2.819 0.00510 **
## shannon 0.13713 0.06256 2.192 0.02909 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.431 on 334 degrees of freedom
## Multiple R-squared: 0.1111, Adjusted R-squared: 0.1004
## F-statistic: 10.43 on 4 and 334 DF, p-value: 5.633e-08## log_est_standard_length log_prey_median_um log_total_preys
## 1.338758 1.009469 1.006007
## shannon
## 1.335122
Les caractéristiques de taille et d’abondance des proies expliquent assez bien la variabilité du succès d’alimentation (\(R^2\) = 0.1004402).
On va maintenant vérifier avec des modèles mixtes l’influence possible de l’hétérogénéité régionale.
## boundary (singular) fit: see ?isSingular## Warning: Model failed to converge with 1 negative eigenvalue: -2.5e-01## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log_feeding_success ~ shannon + log_est_standard_length + log_prey_median_um +
## log_total_preys + (shannon + log_est_standard_length + log_prey_median_um +
## log_total_preys | region)
## Data: prey_matrix_comb2
##
## REML criterion at convergence: 352.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.92178 -0.57253 0.06354 0.61426 2.50164
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 1.83940 1.3562
## shannon 0.02119 0.1456 0.31
## log_est_standard_length 0.26108 0.5110 -0.98 -0.49
## log_prey_median_um 0.16328 0.4041 -0.97 -0.50 0.99
## log_total_preys 0.01789 0.1337 0.36 0.45 -0.42 -0.51
## Residual 0.14599 0.3821
## Number of obs: 339, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -2.86190 0.57940 9.10464 -4.939 0.000776 ***
## shannon 0.18578 0.07733 6.77509 2.403 0.048441 *
## log_est_standard_length 0.53045 0.24743 9.05813 2.144 0.060448 .
## log_prey_median_um -0.28423 0.17283 9.41042 -1.645 0.132996
## log_total_preys -0.12260 0.06702 8.08702 -1.829 0.104324
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) shannn lg_s__ lg_p__
## shannon 0.165
## lg_st_stnd_ -0.810 -0.429
## lg_pry_mdn_ -0.898 -0.251 0.583
## lg_ttl_prys 0.088 0.247 -0.158 -0.312
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Warning: Can't compute random effect variances. Some variance components equal zero. Your model may suffer from singulariy.
## Solution: Respecify random structure!
## You may also decrease the 'tolerance' level to enforce the calculation of random effect variances.## [1] NA## boundary (singular) fit: see ?isSingular## Warning: Model failed to converge with 1 negative eigenvalue: -1.0e+00## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.110252 (tol = 0.002, component 1)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0133512 (tol = 0.002, component 1)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0285016 (tol = 0.002, component 1)## ANOVA-like table for random-effects: Single term deletions
##
## Model:
## log_feeding_success ~ shannon + log_est_standard_length + log_prey_median_um + log_total_preys + (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region)
## npar
## <none> 21
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 16
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 16
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 16
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 16
## logLik
## <none> -176.15
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) -177.66
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) -179.78
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) -184.18
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) -178.00
## AIC
## <none> 394.30
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 387.32
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 391.57
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 400.36
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 387.99
## LRT
## <none>
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 3.0203
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 7.2644
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 16.0601
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 3.6893
## Df
## <none>
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 5
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 5
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 5
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 5
## Pr(>Chisq)
## <none>
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 0.696862
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 0.201706
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 0.006675
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) 0.594953
##
## <none>
## shannon in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region)
## log_est_standard_length in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region)
## log_prey_median_um in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region) **
## log_total_preys in (shannon + log_est_standard_length + log_prey_median_um + log_total_preys | region)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log_feeding_success ~ shannon + log_est_standard_length + log_prey_median_um +
## log_total_preys + (log_prey_median_um | region)
## Data: prey_matrix_comb2
##
## REML criterion at convergence: 366.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.7777 -0.5833 0.0718 0.6374 2.4141
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 0.5777 0.7601
## log_prey_median_um 0.1363 0.3693 -1.00
## Residual 0.1582 0.3977
## Number of obs: 339, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -2.78566 0.42145 20.08372 -6.610 1.9e-06 ***
## shannon 0.19118 0.05918 331.05872 3.230 0.00136 **
## log_est_standard_length 0.39869 0.16936 195.02338 2.354 0.01956 *
## log_prey_median_um -0.27889 0.16347 9.35591 -1.706 0.12090
## log_total_preys -0.08972 0.04778 312.85194 -1.878 0.06133 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) shannn lg_s__ lg_p__
## shannon 0.033
## lg_st_stnd_ -0.432 -0.439
## lg_pry_mdn_ -0.855 0.022 -0.018
## lg_ttl_prys -0.252 0.022 0.142 -0.005
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Warning: Can't compute random effect variances. Some variance components equal zero. Your model may suffer from singulariy.
## Solution: Respecify random structure!
## You may also decrease the 'tolerance' level to enforce the calculation of random effect variances.## [1] NA## # R2 for Mixed Models
##
## Conditional R2: 0.262
## Marginal R2: 0.118## [[1]]## `geom_smooth()` using formula 'y ~ x'
##
## [[2]]
## [[2]]$region## `geom_smooth()` using formula 'y ~ x'
##
##
## [[3]]
##
## [[4]]## `geom_smooth()` using formula 'y ~ x'
Ajouter les régions comme effet aléatoire permet de tenir compte de la variabilité de l’abondance totale de proies et la taille des larves sur le succès alimentaire selon les régions.
Succès alimentaire et composition des proies
On vérifie la relation entre le «feeding success» et la composition des proies.
## Start: AIC=-533.74
## log_feeding_success ~ 1
##
## Df Sum of Sq RSS AIC
## + log_calanus.sp.n 1 13.2476 56.554 -603.08
## + log_pseudocalanus.sp.c 1 11.6448 58.157 -593.61
## + log_other.calanus.sp.c 1 11.0177 58.784 -589.97
## + log_calanus.glacialis.c 1 9.8083 59.993 -583.07
## + log_other.calanoid.sp.c 1 5.9967 63.805 -562.19
## + log_pseudocalanus.sp.n 1 4.4494 65.352 -554.06
## + log_est_standard_length 1 3.4050 66.397 -548.69
## + log_egg 1 1.7610 68.041 -540.40
## + log_appendicularia 1 0.5802 69.221 -534.57
## + log_cyclopoidae.sp.c 1 0.5310 69.271 -534.32
## <none> 69.802 -533.74
## + log_other 1 0.3114 69.490 -533.25
## + log_other.copepodite.and.n 1 0.0494 69.752 -531.98
##
## Step: AIC=-603.08
## log_feeding_success ~ log_calanus.sp.n
##
## Df Sum of Sq RSS AIC
## + log_other.calanus.sp.c 1 10.3309 46.223 -669.46
## + log_calanus.glacialis.c 1 8.2003 48.354 -654.19
## + log_pseudocalanus.sp.c 1 4.3782 52.176 -628.40
## + log_other.calanoid.sp.c 1 2.9028 53.651 -618.95
## + log_est_standard_length 1 2.1060 54.448 -613.95
## + log_other.copepodite.and.n 1 1.0663 55.488 -607.54
## + log_cyclopoidae.sp.c 1 0.5545 55.999 -604.42
## + log_pseudocalanus.sp.n 1 0.5294 56.025 -604.27
## + log_egg 1 0.4900 56.064 -604.03
## <none> 56.554 -603.08
## + log_other 1 0.1243 56.430 -601.83
## + log_appendicularia 1 0.0267 56.527 -601.24
## - log_calanus.sp.n 1 13.2476 69.802 -533.74
##
## Step: AIC=-669.46
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c
##
## Df Sum of Sq RSS AIC
## + log_calanus.glacialis.c 1 1.7248 44.498 -680.36
## + log_cyclopoidae.sp.c 1 1.6516 44.571 -679.80
## + log_pseudocalanus.sp.c 1 1.3816 44.842 -677.75
## + log_other.copepodite.and.n 1 1.3420 44.881 -677.45
## + log_egg 1 0.7877 45.435 -673.29
## + log_other.calanoid.sp.c 1 0.6886 45.534 -672.55
## <none> 46.223 -669.46
## + log_est_standard_length 1 0.2522 45.971 -669.32
## + log_appendicularia 1 0.0254 46.198 -667.65
## + log_pseudocalanus.sp.n 1 0.0124 46.211 -667.56
## + log_other 1 0.0068 46.216 -667.51
## - log_other.calanus.sp.c 1 10.3309 56.554 -603.08
## - log_calanus.sp.n 1 12.5608 58.784 -589.97
##
## Step: AIC=-680.36
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c
##
## Df Sum of Sq RSS AIC
## + log_cyclopoidae.sp.c 1 2.0476 42.451 -694.33
## + log_est_standard_length 1 1.4976 43.001 -689.96
## + log_other.copepodite.and.n 1 1.2758 43.222 -688.22
## + log_egg 1 0.6501 43.848 -683.35
## + log_pseudocalanus.sp.c 1 0.5441 43.954 -682.53
## + log_other.calanoid.sp.c 1 0.3675 44.131 -681.17
## <none> 44.498 -680.36
## + log_other 1 0.1577 44.341 -679.56
## + log_appendicularia 1 0.0006 44.498 -678.36
## + log_pseudocalanus.sp.n 1 0.0002 44.498 -678.36
## - log_calanus.glacialis.c 1 1.7248 46.223 -669.46
## - log_other.calanus.sp.c 1 3.8554 48.354 -654.19
## - log_calanus.sp.n 1 11.8392 56.337 -602.38
##
## Step: AIC=-694.33
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c
##
## Df Sum of Sq RSS AIC
## + log_egg 1 1.5050 40.946 -704.56
## + log_pseudocalanus.sp.c 1 1.3338 41.117 -703.15
## + log_other.copepodite.and.n 1 0.6690 41.782 -697.71
## + log_other.calanoid.sp.c 1 0.5845 41.866 -697.03
## + log_est_standard_length 1 0.4669 41.984 -696.08
## <none> 42.451 -694.33
## + log_appendicularia 1 0.0652 42.385 -692.85
## + log_other 1 0.0393 42.411 -692.64
## + log_pseudocalanus.sp.n 1 0.0005 42.450 -692.33
## - log_cyclopoidae.sp.c 1 2.0476 44.498 -680.36
## - log_calanus.glacialis.c 1 2.1208 44.571 -679.80
## - log_other.calanus.sp.c 1 4.2939 46.745 -663.66
## - log_calanus.sp.n 1 13.8868 56.337 -600.38
##
## Step: AIC=-704.56
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c + log_egg
##
## Df Sum of Sq RSS AIC
## + log_pseudocalanus.sp.c 1 0.8644 40.081 -709.80
## + log_est_standard_length 1 0.7559 40.190 -708.88
## + log_other.copepodite.and.n 1 0.5389 40.407 -707.05
## + log_other.calanoid.sp.c 1 0.4781 40.468 -706.54
## <none> 40.946 -704.56
## + log_other 1 0.0437 40.902 -702.92
## + log_appendicularia 1 0.0281 40.918 -702.80
## + log_pseudocalanus.sp.n 1 0.0065 40.939 -702.62
## - log_egg 1 1.5050 42.451 -694.33
## - log_calanus.glacialis.c 1 1.9898 42.935 -690.48
## - log_cyclopoidae.sp.c 1 2.9025 43.848 -683.35
## - log_other.calanus.sp.c 1 4.8045 45.750 -668.95
## - log_calanus.sp.n 1 13.2667 54.212 -611.42
##
## Step: AIC=-709.8
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c + log_egg +
## log_pseudocalanus.sp.c
##
## Df Sum of Sq RSS AIC
## + log_est_standard_length 1 0.8679 39.213 -715.22
## + log_other.copepodite.and.n 1 0.5256 39.556 -712.27
## <none> 40.081 -709.80
## + log_other.calanoid.sp.c 1 0.1976 39.884 -709.47
## + log_other 1 0.0577 40.024 -708.28
## + log_appendicularia 1 0.0357 40.046 -708.10
## + log_pseudocalanus.sp.n 1 0.0163 40.065 -707.93
## - log_pseudocalanus.sp.c 1 0.8644 40.946 -704.56
## - log_calanus.glacialis.c 1 0.9593 41.041 -703.78
## - log_egg 1 1.0357 41.117 -703.15
## - log_cyclopoidae.sp.c 1 3.4636 43.545 -683.70
## - log_other.calanus.sp.c 1 4.5162 44.597 -675.60
## - log_calanus.sp.n 1 9.8824 49.964 -637.09
##
## Step: AIC=-715.22
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c + log_egg +
## log_pseudocalanus.sp.c + log_est_standard_length
##
## Df Sum of Sq RSS AIC
## + log_other.copepodite.and.n 1 0.4500 38.763 -717.13
## + log_other.calanoid.sp.c 1 0.4203 38.793 -716.87
## <none> 39.213 -715.22
## + log_appendicularia 1 0.1306 39.083 -714.35
## + log_pseudocalanus.sp.n 1 0.0508 39.163 -713.66
## + log_other 1 0.0044 39.209 -713.26
## - log_est_standard_length 1 0.8679 40.081 -709.80
## - log_pseudocalanus.sp.c 1 0.9764 40.190 -708.88
## - log_egg 1 1.2758 40.489 -706.36
## - log_calanus.glacialis.c 1 1.6239 40.837 -703.46
## - log_cyclopoidae.sp.c 1 1.9330 41.146 -700.91
## - log_other.calanus.sp.c 1 5.3789 44.592 -673.64
## - log_calanus.sp.n 1 9.1366 48.350 -646.21
##
## Step: AIC=-717.13
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c + log_egg +
## log_pseudocalanus.sp.c + log_est_standard_length + log_other.copepodite.and.n
##
## Df Sum of Sq RSS AIC
## + log_other.calanoid.sp.c 1 0.3750 38.388 -718.43
## <none> 38.763 -717.13
## + log_appendicularia 1 0.1572 38.606 -716.51
## + log_other 1 0.0185 38.745 -715.29
## - log_other.copepodite.and.n 1 0.4500 39.213 -715.22
## + log_pseudocalanus.sp.n 1 0.0043 38.759 -715.17
## - log_est_standard_length 1 0.7923 39.556 -712.27
## - log_pseudocalanus.sp.c 1 0.9581 39.722 -710.85
## - log_egg 1 1.1600 39.923 -709.13
## - log_cyclopoidae.sp.c 1 1.4983 40.262 -706.27
## - log_calanus.glacialis.c 1 1.5178 40.281 -706.11
## - log_other.calanus.sp.c 1 5.3663 44.130 -675.18
## - log_calanus.sp.n 1 9.5843 48.348 -644.23
##
## Step: AIC=-718.43
## log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c + log_egg +
## log_pseudocalanus.sp.c + log_est_standard_length + log_other.copepodite.and.n +
## log_other.calanoid.sp.c
##
## Df Sum of Sq RSS AIC
## <none> 38.388 -718.43
## + log_appendicularia 1 0.1309 38.257 -717.58
## - log_other.calanoid.sp.c 1 0.3750 38.763 -717.13
## - log_other.copepodite.and.n 1 0.4047 38.793 -716.87
## + log_other 1 0.0446 38.344 -716.82
## + log_pseudocalanus.sp.n 1 0.0150 38.373 -716.56
## - log_pseudocalanus.sp.c 1 0.5924 38.981 -715.23
## - log_est_standard_length 1 0.9953 39.384 -711.75
## - log_egg 1 1.1963 39.585 -710.02
## - log_cyclopoidae.sp.c 1 1.4399 39.828 -707.94
## - log_calanus.glacialis.c 1 1.5720 39.960 -706.82
## - log_other.calanus.sp.c 1 5.2131 43.601 -677.26
## - log_calanus.sp.n 1 9.1880 47.576 -647.68##
## Call:
## lm(formula = log_feeding_success ~ log_calanus.sp.n + log_other.calanus.sp.c +
## log_calanus.glacialis.c + log_cyclopoidae.sp.c + log_egg +
## log_pseudocalanus.sp.c + log_est_standard_length + log_other.copepodite.and.n +
## log_other.calanoid.sp.c, data = prey_matrix_comb2)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.12309 -0.20112 0.01735 0.19538 1.71692
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -2.81275 0.19166 -14.676 < 2e-16 ***
## log_calanus.sp.n 0.35991 0.04056 8.874 < 2e-16 ***
## log_other.calanus.sp.c 0.45449 0.06800 6.684 9.95e-11 ***
## log_calanus.glacialis.c 0.25024 0.06818 3.671 0.000282 ***
## log_cyclopoidae.sp.c -0.14819 0.04219 -3.513 0.000505 ***
## log_egg 0.10956 0.03421 3.202 0.001498 **
## log_pseudocalanus.sp.c 0.10851 0.04815 2.253 0.024902 *
## log_est_standard_length -0.50203 0.17189 -2.921 0.003735 **
## log_other.copepodite.and.n -0.09475 0.05087 -1.862 0.063436 .
## log_other.calanoid.sp.c 0.10619 0.05924 1.793 0.073932 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.3416 on 329 degrees of freedom
## Multiple R-squared: 0.45, Adjusted R-squared: 0.435
## F-statistic: 29.91 on 9 and 329 DF, p-value: < 2.2e-16## log_calanus.sp.n log_other.calanus.sp.c
## 1.427345 1.707410
## log_calanus.glacialis.c log_cyclopoidae.sp.c
## 2.023095 1.660537
## log_egg log_pseudocalanus.sp.c
## 1.189876 1.881641
## log_est_standard_length log_other.copepodite.and.n
## 2.498614 1.202233
## log_other.calanoid.sp.c
## 1.361700
Les caractéristiques taxonomiques des proies expliquent bien la variabilité du succès d’alimentation (\(R^2\) = 0.4349915).
On va maintenant vérifier avec des modèles mixtes l’influence possible de l’hétérogénéité régionale.
## boundary (singular) fit: see ?isSingular## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log_feeding_success ~ log_est_standard_length + log_calanus.glacialis.c +
## log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c +
## log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c +
## (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n +
## log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c +
## log_other.copepodite.and.n + log_other.calanoid.sp.c +
## log_pseudocalanus.sp.c | region)
## Data: prey_matrix_comb2
##
## REML criterion at convergence: 133.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.0020 -0.5811 0.0347 0.5558 4.9207
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 0.239021 0.48890
## log_est_standard_length 0.339305 0.58250 -0.85
## log_calanus.glacialis.c 0.088039 0.29671 0.08 -0.53
## log_calanus.sp.n 0.118143 0.34372 0.41 -0.82 0.88
## log_cyclopoidae.sp.c 0.014584 0.12076 -0.32 0.01 0.60 0.37
## log_egg 0.010147 0.10073 0.54 -0.69 0.57 0.66
## log_other.calanus.sp.c 0.025268 0.15896 -0.33 0.71 -0.81 -0.89
## log_other.copepodite.and.n 0.015111 0.12293 -0.89 0.69 -0.12 -0.29
## log_other.calanoid.sp.c 0.037510 0.19367 -0.59 0.20 0.54 0.30
## log_pseudocalanus.sp.c 0.009112 0.09545 0.42 0.06 -0.59 -0.52
## Residual 0.064843 0.25464
##
##
##
##
##
##
## -0.29
## -0.68 -0.29
## 0.44 -0.72 0.11
## 0.92 -0.37 -0.54 0.70
## -0.78 0.20 0.68 -0.64 -0.91
##
## Number of obs: 339, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -2.47732 0.24335 6.68870 -10.180 2.58e-05 ***
## log_est_standard_length -0.88258 0.25234 6.71283 -3.498 0.0107 *
## log_calanus.glacialis.c 0.39541 0.11690 4.69659 3.383 0.0216 *
## log_calanus.sp.n 0.32496 0.11983 7.73152 2.712 0.0274 *
## log_cyclopoidae.sp.c -0.09275 0.05611 9.92003 -1.653 0.1296
## log_egg 0.12543 0.04471 7.95660 2.805 0.0231 *
## log_other.calanus.sp.c 0.32638 0.07849 7.65388 4.158 0.0035 **
## log_other.copepodite.and.n 0.04321 0.05881 8.71229 0.735 0.4818
## log_other.calanoid.sp.c 0.13131 0.08187 7.69462 1.604 0.1489
## log_pseudocalanus.sp.c 0.18404 0.05254 5.98695 3.503 0.0128 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ lg_clns.g. lg_clns.s. lg_cy.. log_gg lg_thr.clns..
## lg_st_stnd_ -0.898
## lg_clns.gl. 0.169 -0.462
## lg_clns.sp. 0.232 -0.603 0.719
## lg_cyclpd.. 0.013 -0.139 0.410 0.217
## log_egg 0.304 -0.464 0.431 0.481 -0.245
## lg_thr.clns.. -0.045 0.265 -0.581 -0.560 -0.300 -0.096
## lg_thr.cp.. -0.455 0.374 -0.052 -0.249 0.149 -0.374 0.032
## lg_thr.clnd.. -0.238 0.046 0.387 0.217 0.537 -0.235 -0.343
## lg_psdcln.. 0.162 0.046 -0.397 -0.365 -0.484 0.053 0.218
## lg_thr.cp.. lg_thr.clnd..
## lg_st_stnd_
## lg_clns.gl.
## lg_clns.sp.
## lg_cyclpd..
## log_egg
## lg_thr.clns..
## lg_thr.cp..
## lg_thr.clnd.. 0.444
## lg_psdcln.. -0.284 -0.583
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Warning: Can't compute random effect variances. Some variance components equal zero. Your model may suffer from singulariy.
## Solution: Respecify random structure!
## You may also decrease the 'tolerance' level to enforce the calculation of random effect variances.## [1] NA## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0645145 (tol = 0.002, component 1)## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular## Warning: Model failed to converge with 1 negative eigenvalue: -3.0e-02## boundary (singular) fit: see ?isSingular## Warning: Model failed to converge with 1 negative eigenvalue: -1.3e-01## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular## ANOVA-like table for random-effects: Single term deletions
##
## Model:
## log_feeding_success ~ log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c + (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## npar
## <none> 66
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 56
## logLik
## <none> -66.680
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -71.243
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -72.631
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -98.093
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -70.519
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -71.357
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -69.531
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -69.976
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -72.269
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) -68.513
## AIC
## <none> 265.36
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 254.49
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 257.26
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 308.19
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 253.04
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 254.72
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 251.06
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 251.95
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 256.54
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 249.03
## LRT
## <none>
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 9.127
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 11.902
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 62.827
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 7.679
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 9.355
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 5.703
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 6.593
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 11.178
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 3.667
## Df
## <none>
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 10
## Pr(>Chisq)
## <none>
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.5201
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.2917
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 1.053e-09
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.6601
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.4987
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.8395
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.7632
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.3438
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) 0.9611
##
## <none>
## log_est_standard_length in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_calanus.glacialis.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_calanus.sp.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region) ***
## log_cyclopoidae.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_egg in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_other.calanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_other.copepodite.and.n in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_other.calanoid.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## log_pseudocalanus.sp.c in (log_est_standard_length + log_calanus.glacialis.c + log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c + log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c | region)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula:
## log_feeding_success ~ log_est_standard_length + log_calanus.glacialis.c +
## log_calanus.sp.n + log_cyclopoidae.sp.c + log_egg + log_other.calanus.sp.c +
## log_other.copepodite.and.n + log_other.calanoid.sp.c + log_pseudocalanus.sp.c +
## (log_calanus.sp.n | region)
## Data: prey_matrix_comb2
##
## REML criterion at convergence: 180.3
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.2803 -0.5671 0.0442 0.5756 4.9586
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 0.09946 0.3154
## log_calanus.sp.n 0.09541 0.3089 -0.94
## Residual 0.08155 0.2856
## Number of obs: 339, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -2.49157 0.21611 83.37079 -11.529 < 2e-16 ***
## log_est_standard_length -0.79308 0.16603 304.81440 -4.777 2.77e-06 ***
## log_calanus.glacialis.c 0.29061 0.06061 322.53759 4.795 2.49e-06 ***
## log_calanus.sp.n 0.30870 0.11020 8.59700 2.801 0.021586 *
## log_cyclopoidae.sp.c -0.11054 0.04194 247.56276 -2.636 0.008923 **
## log_egg 0.10471 0.02995 322.19952 3.497 0.000537 ***
## log_other.calanus.sp.c 0.40108 0.06105 304.49520 6.569 2.18e-10 ***
## log_other.copepodite.and.n 0.02501 0.04540 322.75502 0.551 0.582174
## log_other.calanoid.sp.c 0.11641 0.05098 321.71679 2.283 0.023068 *
## log_pseudocalanus.sp.c 0.14308 0.04445 312.77826 3.219 0.001422 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ lg_clns.g. lg_clns.s. lg_cy.. log_gg lg_thr.clns..
## lg_st_stnd_ -0.851
## lg_clns.gl. 0.330 -0.401
## lg_clns.sp. -0.488 0.027 -0.003
## lg_cyclpd.. 0.230 -0.272 0.121 -0.075
## log_egg 0.020 -0.109 0.126 0.000 -0.182
## lg_thr.clns.. 0.201 -0.284 -0.293 0.034 0.116 0.099
## lg_thr.cp.. 0.031 -0.079 0.049 -0.099 -0.183 0.046 -0.041
## lg_thr.clnd.. 0.211 -0.254 0.081 -0.022 -0.013 0.056 -0.072
## lg_psdcln.. -0.038 0.048 -0.282 -0.090 -0.243 -0.146 -0.102
## lg_thr.cp.. lg_thr.clnd..
## lg_st_stnd_
## lg_clns.gl.
## lg_clns.sp.
## lg_cyclpd..
## log_egg
## lg_thr.clns..
## lg_thr.cp..
## lg_thr.clnd.. 0.058
## lg_psdcln.. 0.063 -0.254## # Intraclass Correlation Coefficient
##
## Adjusted ICC: 0.338
## Conditional ICC: 0.200## # R2 for Mixed Models
##
## Conditional R2: 0.608
## Marginal R2: 0.407## [[1]]## `geom_smooth()` using formula 'y ~ x'
##
## [[2]]
## [[2]]$region## `geom_smooth()` using formula 'y ~ x'
##
##
## [[3]]
##
## [[4]]## `geom_smooth()` using formula 'y ~ x'
Ajouter les régions comme effet aléatoire permet de tenir compte de la variabilité de l’abondance des nauplii de Calanus sp parmi les proies sur le succès alimentaire selon les régions.
Section 3. Généralisme/spécialisme et environnement
Je trouve l’index de Shannon plus facile conceptuellement à comprendre et on peut comparer au niveau de l’individu, contrairement à Levins’ pour lequel il faut absolument comparer des groupes. Je consière au départ chaque poisson comme un site distinct qui partage des caractéristiques avec des poissons pêchés des mêmes régions (un peu comme un site dans une forêt et un site avoisinant se ressembleront dans leur composition, mais on peut les comparer quand même).
## Régressions linéaires (encore sans MS2010)
## Start: AIC=-580.16
## shannon ~ 1
##
## Df Sum of Sq RSS AIC
## + log_est_standard_length 1 7.1725 46.093 -624.88
## + open_water_day 1 2.6371 50.629 -594.56
## + log_indstandard 1 1.7342 51.531 -588.85
## + surf_sal_kgm3 1 1.4109 51.855 -586.83
## + log_NASC_zoo 1 0.9420 52.324 -583.93
## + surf_temp_degC 1 0.6222 52.643 -581.96
## <none> 53.266 -580.16
##
## Step: AIC=-624.88
## shannon ~ log_est_standard_length
##
## Df Sum of Sq RSS AIC
## + surf_sal_kgm3 1 0.4022 45.691 -625.71
## + log_indstandard 1 0.3772 45.716 -625.53
## <none> 46.093 -624.88
## + log_NASC_zoo 1 0.1572 45.936 -623.98
## + surf_temp_degC 1 0.1133 45.980 -623.67
## + open_water_day 1 0.0265 46.067 -623.06
## - log_est_standard_length 1 7.1725 53.266 -580.16
##
## Step: AIC=-625.71
## shannon ~ log_est_standard_length + surf_sal_kgm3
##
## Df Sum of Sq RSS AIC
## + log_indstandard 1 0.9594 44.732 -630.56
## <none> 45.691 -625.71
## - surf_sal_kgm3 1 0.4022 46.093 -624.88
## + surf_temp_degC 1 0.0325 45.659 -623.94
## + log_NASC_zoo 1 0.0276 45.663 -623.90
## + open_water_day 1 0.0186 45.672 -623.84
## - log_est_standard_length 1 6.1637 51.855 -586.83
##
## Step: AIC=-630.56
## shannon ~ log_est_standard_length + surf_sal_kgm3 + log_indstandard
##
## Df Sum of Sq RSS AIC
## <none> 44.732 -630.56
## + surf_temp_degC 1 0.2378 44.494 -630.28
## + open_water_day 1 0.0515 44.680 -628.93
## + log_NASC_zoo 1 0.0001 44.732 -628.56
## - log_indstandard 1 0.9594 45.691 -625.71
## - surf_sal_kgm3 1 0.9843 45.716 -625.53
## - log_est_standard_length 1 3.7403 48.472 -606.62## Step Df Deviance Resid. Df Resid. Dev AIC
## 1 NA NA 322 53.26563 -580.1626
## 2 + log_est_standard_length -1 7.1724543 321 46.09317 -624.8770
## 3 + surf_sal_kgm3 -1 0.4021707 320 45.69100 -625.7076
## 4 + log_indstandard -1 0.9593697 319 44.73163 -630.5618##
## Call:
## lm(formula = shannon ~ log_est_standard_length + surf_sal_kgm3 +
## log_indstandard, data = shannonData)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.20424 -0.19330 0.03865 0.25350 0.80619
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.266491 0.227707 -1.170 0.24274
## log_est_standard_length 0.716004 0.138636 5.165 4.25e-07 ***
## surf_sal_kgm3 0.019170 0.007236 2.649 0.00846 **
## log_indstandard -0.081151 0.031025 -2.616 0.00933 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.3745 on 319 degrees of freedom
## Multiple R-squared: 0.1602, Adjusted R-squared: 0.1523
## F-statistic: 20.29 on 3 and 319 DF, p-value: 4.665e-12## log_est_standard_length surf_sal_kgm3 log_indstandard
## 1.218578 1.281460 1.320773
## boundary (singular) fit: see ?isSingular## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: shannon ~ log_est_standard_length + log_indstandard + surf_sal_kgm3 +
## (log_est_standard_length + log_indstandard + surf_sal_kgm3 |
## region)
## Data: shannonData
##
## REML criterion at convergence: 270.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.79888 -0.59620 0.02988 0.69494 2.21006
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## region (Intercept) 0.648312 0.80518
## log_est_standard_length 0.148682 0.38559 -0.46
## log_indstandard 0.027938 0.16715 -0.86 0.62
## surf_sal_kgm3 0.001104 0.03323 -0.93 0.11 0.74
## Residual 0.118882 0.34479
## Number of obs: 323, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.095467 0.412741 1.535712 0.231 0.8441
## log_est_standard_length 0.984125 0.208737 1.746338 4.715 0.0544 .
## log_indstandard -0.088952 0.070358 4.658434 -1.264 0.2657
## surf_sal_kgm3 -0.004959 0.015322 1.081625 -0.324 0.7975
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ lg_nds
## lg_st_stnd_ -0.386
## lg_ndstndrd -0.410 0.459
## srf_sl_kgm3 -0.866 -0.072 0.395
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Warning: Can't compute random effect variances. Some variance components equal zero. Your model may suffer from singulariy.
## Solution: Respecify random structure!
## You may also decrease the 'tolerance' level to enforce the calculation of random effect variances.## [1] NA## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular
## boundary (singular) fit: see ?isSingular## ANOVA-like table for random-effects: Single term deletions
##
## Model:
## shannon ~ log_est_standard_length + log_indstandard + surf_sal_kgm3 + (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region)
## npar
## <none> 15
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 11
## log_indstandard in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 11
## surf_sal_kgm3 in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 11
## logLik
## <none> -135.21
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) -135.71
## log_indstandard in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) -138.75
## surf_sal_kgm3 in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) -136.22
## AIC
## <none> 300.43
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 293.43
## log_indstandard in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 299.50
## surf_sal_kgm3 in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 294.44
## LRT
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 1.0000
## log_indstandard in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 7.0729
## surf_sal_kgm3 in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 2.0127
## Df
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 4
## log_indstandard in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 4
## surf_sal_kgm3 in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 4
## Pr(>Chisq)
## <none>
## log_est_standard_length in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 0.9098
## log_indstandard in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 0.1321
## surf_sal_kgm3 in (log_est_standard_length + log_indstandard + surf_sal_kgm3 | region) 0.7334## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: shannon ~ log_est_standard_length + log_indstandard + surf_sal_kgm3 +
## (1 | region)
## Data: shannonData
##
## REML criterion at convergence: 291.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.88215 -0.54685 0.07735 0.74046 2.09304
##
## Random effects:
## Groups Name Variance Std.Dev.
## region (Intercept) 0.01117 0.1057
## Residual 0.13286 0.3645
## Number of obs: 323, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -0.288618 0.296161 81.961949 -0.975 0.33266
## log_est_standard_length 0.839748 0.150291 219.404846 5.587 6.79e-08 ***
## log_indstandard -0.123990 0.037698 74.464484 -3.289 0.00154 **
## surf_sal_kgm3 0.012041 0.008995 112.234179 1.339 0.18337
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ lg_nds
## lg_st_stnd_ -0.407
## lg_ndstndrd 0.233 0.248
## srf_sl_kgm3 -0.791 -0.189 -0.221## # Intraclass Correlation Coefficient
##
## Adjusted ICC: 0.078
## Conditional ICC: 0.062## # R2 for Mixed Models
##
## Conditional R2: 0.267
## Marginal R2: 0.205
Figures
Section 1.
PCA des régions-années, et relations entre l’environnement et l’abondance de zoo et de larves
Carbone et taille, taille et OWD
Succès alimentaire ~ taille + environnement (variables dans modèles)
Section 2.
Succès et mesures proies
Composition générale diète
Succès et composition proies
Section 3. Généralisme et FS
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: shannon ~ log_est_standard_length + log_indstandard + surf_sal_kgm3 +
## (1 | region)
## Data: shannonData
##
## REML criterion at convergence: 291.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.88215 -0.54685 0.07735 0.74046 2.09304
##
## Random effects:
## Groups Name Variance Std.Dev.
## region (Intercept) 0.01117 0.1057
## Residual 0.13286 0.3645
## Number of obs: 323, groups: region, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) -0.288618 0.296161 81.961949 -0.975 0.33266
## log_est_standard_length 0.839748 0.150291 219.404846 5.587 6.79e-08 ***
## log_indstandard -0.123990 0.037698 74.464484 -3.289 0.00154 **
## surf_sal_kgm3 0.012041 0.008995 112.234179 1.339 0.18337
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) lg_s__ lg_nds
## lg_st_stnd_ -0.407
## lg_ndstndrd 0.233 0.248
## srf_sl_kgm3 -0.791 -0.189 -0.221